a2m2html output for file tmp.a2m

Citations (SAM, SAM-T99, HMMs)

R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1999.
A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.

Sequence numbers correspond to the following labels:

- T0110 Protein HI1288, H. influenzae
- gi|140742|sp|P09170|RBFA_ECOLI_3:129 RIBOSOME-BINDING FACTOR A (P15B PROTEIN) (Escherichia coli)
- gi|76180|pir||Q9EC15 ribosome-binding factor rbfA - Escherichia coli (Escherichia coli)
- gi|42218|emb|CAA32020.1| (X13775) P15B gene product (AA 1 - 133) [Escherichia coli] (Escherichia coli)
- gi|42222|emb|CAA31634.1| (X13270) P15B gene product (AA 1 - 133) [Escherichia coli] (Escherichia coli)
- gi|606107|gb|AAA57970.1| (U18997) P15B [Escherichia coli] (Escherichia coli)
- gi|1789558|gb|AAC76201.1| (AE000397) ribosome-binding factor A [Escherichia coli] (Escherichia coli)
- gi|1172847|sp|P45141|RBFA_HAEIN_2:127 RIBOSOME-BINDING FACTOR A (Haemophilus influenzae)
- gi|1074716|pir||A64170 ribosome-binding factor A - Haemophilus influenzae (strain Rd KW20) (Haemophilus influenzae)
- gi|1574747|gb|AAC22937.1| (U32809) ribosome binding factor A (rbfA) [Haemophilus influenzae Rd] (Haemophilus influenzae Rd)
- gi|3914553|sp|O34272|RBFA_YEREN_3:127 RIBOSOME-BINDING FACTOR A (Yersinia enterocolitica)
- gi|2462713|emb|CAA71698.1| (Y10692) yhbB [Yersinia enterocolitica] (Yersinia enterocolitica)
- gi|3914548|sp|O05340|RBFA_STIAU_1:115 RIBOSOME-BINDING FACTOR A (Stigmatella aurantiaca)
- gi|1934985|emb|CAA61164.1| (X87940) ribosome binding factor A [Stigmatella aurantiaca] (Stigmatella aurantiaca)
- gi|418464|sp|P32731|RBFA_BACSU_3:114 RIBOSOME-BINDING FACTOR A (P15B PROTEIN) (Bacillus subtilis)
- gi|541418|pir||G36905 ribosome-binding factor A rbfA - Bacillus subtilis (Bacillus subtilis)
- gi|580902|emb|CAA79236.1| (Z18631) ORF6 [Bacillus subtilis] (Bacillus subtilis)
- gi|2634037|emb|CAB13538.1| (Z99112) ribosome-binding factor A [Bacillus subtilis] (Bacillus subtilis)
- gi|3914560|sp|Q55625|RBFA_SYNY3_1:127 RIBOSOME-BINDING FACTOR A (Synechocystis PCC6803)
- gi|7444620|pir||S76285 hypothetical protein - Synechocystis sp. (strain PCC 6803) (Synechocystis sp.)
- gi|1001511|dbj|BAA10137.1| (D64000) hypothetical protein [Synechocystis sp.] (Synechocystis sp.)
- gi|7444622|pir||H72324_1:123 ribosome binding factor A - Thermotoga maritima (strain MSB8) (Thermotoga maritima)
- gi|4981389|gb|AAD35937.1|AE001752_4 (AE001752) ribosome binding factor A [Thermotoga maritima] (Thermotoga maritima)
- gi|8163433|gb|AAF73669.1|_21:138 (AE002205) ribosome-binding factor A [Chlamydophila pneumoniae AR39] (Chlamydophila pneumoniae AR39)
- gi|6225917|sp|Q9Z5I8|RBFA_MYCLE_1:119 PROBABLE RIBOSOME-BINDING FACTOR A (Mycobacterium leprae)
- gi|4455679|emb|CAB36571.1| (AL035472) putative ribosome-binding factor A [Mycobacterium leprae] (Mycobacterium leprae)
- gi|6685851|sp|Q9Z8M0|RBFA_CHLPN_1:117 RIBOSOME BINDING FACTOR A (Chlamydophila pneumoniae)
- gi|7444624|pir||G72093 ribosome binding factor A - Chlamydia pneumoniae (strain CWL029) (Chlamydophila pneumoniae)
- gi|4376595|gb|AAD18467.1| (AE001616) Ribosome Binding Factor A [Chlamydophila pneumoniae] (Chlamydophila pneumoniae)
- gi|3914556|sp|P71614|RBFA_MYCTU_1:119 PROBABLE RIBOSOME-BINDING FACTOR A (Mycobacterium tuberculosis)
- gi|7478846|pir||A70694 probable rbfA - Mycobacterium tuberculosis (strain H37RV) (Mycobacterium tuberculosis)
- gi|1648882|emb|CAB03671.1| (Z81331) rbfA [Mycobacterium tuberculosis] (Mycobacterium tuberculosis)
- gi|6225918|sp|Q9Z527|RBFA_STRCO_1:119 RIBOSOME-BINDING FACTOR A (Streptomyces coelicolor)
- gi|7481285|pir||T35987 probable ribosome-binding factor - Streptomyces coelicolor (Streptomyces coelicolor)
- gi|4464272|emb|CAB37475.1| (AL035559) putative ribosome-binding factor [Streptomyces coelicolor A3(2)] (Streptomyces coelicolor A3(2))
- gi|6093904|sp|O83860|RBFA_TREPA_3:118 RIBOSOME-BINDING FACTOR A (Treponema pallidum)
- gi|7521391|pir||G71269 probable ribosome-binding factor A (rbfA) - syphilis spirochete (Treponema pallidum subsp. pallidum)
- gi|3323207|gb|AAC26580.1| (AE001258) ribosome-binding factor A (rbfA) [Treponema pallidum] (Treponema pallidum)
- gi|3914554|sp|O51742|RBFA_BORBU_7:122 RIBOSOME-BINDING FACTOR A (Borrelia burgdorferi)
- gi|7444621|pir||A70200 ribosome-binding factor A (rbfA) homolog - Lyme disease spirochete (Borrelia burgdorferi)
- gi|2688746|gb|AAC67152.1| (AE001179) ribosome-binding factor A (rbfA) [Borrelia burgdorferi] (Borrelia burgdorferi)
- gi|8163212|gb|AAF73551.1|_1:126 (AE002304) ribosome-binding factor A [Chlamydia muridarum] (Chlamydia muridarum)
- gi|7226619|gb|AAF41747.1|_5:119 (AE002485) ribosome-binding factor A [Neisseria meningitidis MC58] (Neisseria meningitidis MC58)
- gi|1723113|sp|P47389|RBFA_MYCGE_2:110 PROBABLE RIBOSOME-BINDING FACTOR A (Mycoplasma genitalium)
- gi|1361568|pir||H64215 hypothetical protein homolog MG143 - Mycoplasma genitalium (Mycoplasma genitalium)
- gi|3844736|gb|AAC71361.1| (U39695) ribosome-binding factor A, putative [Mycoplasma genitalium] (Mycoplasma genitalium)
- gi|7380227|emb|CAB84813.1|_5:119 (AL162756) ribosomal-binding factor A [Neisseria meningitidis] (Neisseria meningitidis)
- gi|2496316|sp|P75589|RBFA_MYCPN_2:114 PROBABLE RIBOSOME-BINDING FACTOR A (Mycoplasma pneumoniae)
- gi|2146640|pir||S74001 ribosome binding factor A - Mycoplasma pneumoniae (strain ATCC 29342) (Mycoplasma pneumoniae)
- gi|1674381|gb|AAB96323.1| (AE000062) Mycoplasma pneumoniae, ribosome binding factor A; similar to Swiss-Prot Accession Number P32731, from E. coli (Mycoplasma pneumoniae)
- gi|3914549|sp|O05964|RBFA_RICPR_6:119 RIBOSOMAL-BINDING FACTOR A (Rickettsia prowazekii)
- gi|7444623|pir||B71702 ribosome-binding factor A (rbfA) RP435 - Rickettsia prowazekii (Rickettsia prowazekii)
- gi|2073498|emb|CAA72443.1| (Y11777) ribosomal binding factor A [Rickettsia prowazekii] (Rickettsia prowazekii)
- gi|3860992|emb|CAA14892.1| (AJ235271) RIBOSOME-BINDING FACTOR A (rbfA) [Rickettsia prowazekii] (Rickettsia prowazekii)
- gi|6685836|sp|O84097|RBFA_CHLTR_1:119 RIBOSOME BINDING FACTOR A (Chlamydia trachomatis)
- gi|7469030|pir||G71558 probable ribosome binding factor A - Chlamydia trachomatis (serotype D, strain UW3/Cx) (Chlamydia trachomatis)
- gi|3328491|gb|AAC67686.1| (AE001283) Ribosome Binding Factor A [Chlamydia trachomatis] (Chlamydia trachomatis)
- gi|3947715|emb|CAA05920.1|_5:120 (AJ003164) ribosome binding factor A [Streptococcus agalactiae] (Streptococcus agalactiae)
- gi|7465302|pir||F71940_3:109 probable ribosome-binding factor A - Helicobacter pylori (strain J99) (Helicobacter pylori)
- gi|4154898|gb|AAD05947.1| (AE001472) putative RIBOSOME-BINDING FACTOR A [Helicobacter pylori J99] (Helicobacter pylori J99)
- gi|7465357|pir||G64650_3:109 ribosome-binding factor A - Helicobacter pylori (strain 26695) (Helicobacter pylori)
- gi|2314194|gb|AAD08092.1| (AE000612) ribosome-binding factor A (rbfA) [Helicobacter pylori 26695] (Helicobacter pylori 26695)
- gi|4583984|emb|CAB40558.1|_1:110 (AJ005118) ribosome binding factor A [Lactococcus lactis] (Lactococcus lactis)
- gi|4586219|emb|CAB40971.1|_1:110 (AJ237898) RBFA, putative [Porphyromonas gingivalis] (Porphyromonas gingivalis)
- gi|6899298|gb|AAF30730.1|AE002129_6_1:113 (AE002129) ribosome binding factor A [Ureaplasma urealyticum] (Ureaplasma urealyticum)
- gi|7496507|pir||T19469_26:136 hypothetical protein C25G4.3 - Caenorhabditis elegans (Caenorhabditis elegans)
- gi|3874417|emb|CAA94572.1| (Z70680) cDNA EST EMBL:T00472 comes from this gene [Caenorhabditis elegans] (Caenorhabditis elegans)
- gi|3914555|sp|O65693|RBFA_ARATH_18:146 PUTATIVE RIBOSOME-BINDING FACTOR A, CHLOROPLAST PRECURSOR (Arabidopsis thaliana)
- gi|7487664|pir||T05293 hypothetical protein T4L20.310 - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|3096942|emb|CAA18852.1| (AL023094) putative protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7270424|emb|CAB80190.1| (AL161586) putative protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7473662|pir||A75463_23:112 probable ribosome-binding factor A - Deinococcus radiodurans (strain R1) (Deinococcus radiodurans)
- gi|6458618|gb|AAF10475.1|AE001942_7 (AE001942) ribosome-binding factor A, putative [Deinococcus radiodurans] (Deinococcus radiodurans)

              10        20              30          40             50  
              |         |               |           |              |  
   1 MAREFKRSDRVAQEIQKEIAVIL.QREV.....KDPRIG..MVTVSDVEVSSDLS.....YAKIF
   2 --KEFGRPQRVAQEMQKEIALIL.QREI.....KDPRLGm.MTTVSGVEMSRDLA.....YAKVY
   3 -AREFKRSDRVAQEIQKEIAVIL.QREV.....KDPRIG..MVTVSDVEVSSDLS.....YAKIF
   4 -----SRSQRVSQEMQKEIALIL.QREI.....KDPRVG..MATVSGIELSRDLA.....YAKVF
   5 -MTTHSRPERVGQEIQAAIGQLLtRGEL.....RDPRIG..FITITGVKVSPDLR.....VAQVF
   6 -----MRANRVGEQMKKELGDII.SRKL.....KDPRIG..FLTVTDVRVSGDLQ.....IAKVY
   7 -MATSRRVSRVSSLIKREVSQML.LHEI.....KDDRVGtgMVSVTEVEVSGDLQ.....HAKIF
   8 -MNPAYRKAMLESEIQKLLMEAL.Q-QL.....RDPRLKkdFVTFSRVELSKDKR.....YADVY
   9 CMTENRRIKRVNALLQEAIAKVI.LKDV.....KHPKISnlWITVTRVSLSKDLH.....SARVY
  10 -MADQARARRLAKRICTIVASAI.EFEI.....KDPGLD..GVTIVDVKVTADLH.....DATVF
  11 -MTENRRIKRVNALLQEAIAKVI.LKDV.....KHPKISnlWITVTRVSLSKDLH.....SARVY
  12 -MADAARARRLAKRIAAIVASAI.EYEI.....KDPGLA..GVTITDAKVTADLH.....DATVY
  13 -MADNARAKRLADLIREVVAQKL.QRGI.....KDPRLGs.HVTITDTRVTGDLR.....EATVF
  14 -QVSQLRVRKLGEHIRAEIAQLImLGKI.....KDPRVSp.FLSVNWVDVSGGMV.....CARVY
  15 FMYKNIKKFKLESFIAQEIGNLIvSGGI.....KDPRIHs.FLTVVKVEFSKDLI.....NAKVF
  16 -MTENRRMKKVNAMLRESIAKVI.LKDV.....KHPKISnrWITITRVSLSRDLQ.....SARVY
  17 -QRGYARQDRVKEQIMRELAELV.RTGL.....KDPRAG..FITVNEVEVTRDYS.....HATVF
  18 ---ASYRKQRIENDIIRLINRTI.INEI.....YDPVVK..LGHVSHVKLSADFF.....HAVVY
  19 -QRGYARQDRVKEQIMRELAELV.RTGL.....KDPRAG..FITVNEVEVTRDYS.....HATVF
  20 ---ASYKKERLENDIIRLINRTV.IHEI.....YNETVK..TGHVTHVKLSDDLL.....HVTVY
  21 -KTNSHRQQKLASIINEVLIEILkRGKM.....LDKRLFdcPLTITKIIVTADLK.....IANCY
  22 -MAENRRMKKVNAMLREAIAKVI.LKDV.....KHPKISnrWITITRVSLSRDLQ.....SACVY
  23 LIMANHRIDRVGMEIKREVNEIL.RLRV.....NDPRVQ..DVTITDVQMLGDLS.....MAKVF
  24 -----AHKERLESNLLELLQEAL.A-SL.....NDSELN..SLSVTKVECSKGKH.....HALVF
  25 -----AHKERLESNLLELLQEAL.A-SL.....NDSELN..SLSVTKVECSKGKH.....HAYVF
  26 -MGNSFRSDRVAVEIQREINDIL.RNKV.....RDPRVQ..DVNITDVQLTGDLS.....QATVY
  27 --MDNKRLSKIERLLQKELSEIF.LRDA.....KSLPGV..IVSVTNVRVSPDLS.....IARIH
  28 -MANEVRVARLESLIKDVINNAL.ANEI.....NDKIAK..LARVTAVRLSNDLS.....VAKIF
  29 -RLDDKKVVQLSRILEERIAEVV.A---.....TDEMLGrlQLQITRVRVDRAFT.....QVSVY
  30 CMANPRRVKMVAKQIMRELSDML.LTDTv13lgADRYLSs.LTTISDVEVSNDLQv12cnVVKVY
  31 --GPLMKPEQVQAQMSRVLSSAI.A-EL.....RDPRVPl.IVTVERVHVTPDYG.....QARVY


                  60        70        80          90       100       11
                  |         |         |           |         |         
   1 VTFLF....D..HDEMAIEQGMKGLEKASPYIRSLLGKAMR..LRIVPEIRFIYDQSLVEGMRMS
   2 VTFLN....D..KDEDAVKAGIKALQEASGFIRSLLGKAMR..LRIVPELTFFYDNSLVEGMRMS
   3 VTFLF....D..HDEMAIEQGMKGLEKASPYIRSLLGKAMR..LRIVPEIRFIYDQSLVEGMRMS
   4 VTFLNvltdN..ADPDTAKNGIKALQDASGYIRTLLGKAMR..LRIVPELTFAYDNSLIEGMRMS
   5 YSMMG....T..--AQERAETQKGLDAAKGFVRREVTAAVN..LRVSPEVFFTFDESVGEGDKID
   6 ISVLG....D..--EKKREEALKGLAKAKGFIRSEIGSRIR..LRKTPEIEFEFDESIDYGNRIE
   7 VSIYG....S..--PEAKASTMAGLHSAAPFVRRELGQRMR..LRRTPEVSFLEDRSLERGDKIL
   8 VSFLG....T..--PEERKETVEILNRAKGFFRTFIAKNLR..LYVAPEIRFYEDKGIEASVKVH
   9 VSVMP....H..--ENTKEEALEALKVSAGFIAHRASKNVV..LKYFPELHFYLDDIFSPQDYIE
  10 YTVMG....RtlEDAPDYTAATAALNRAKGTLRSKVGAGTG..VRFTPTLTFIRDTTSDSVARME
  11 VSVMP....H..--ENTKEEALEALKVSAGFIAHRASKNVV..LKYFPELHFYLDDIFSPQDYIE
  12 YTVMG....RtlHDEPNCAGAAAALERAKGVLRTKVGAGTG..VRFTPTLTFTLDTISDSVHRMD
  13 YTVYG....D..--DEERKAATAGLESAKGILRSEVGKAAG..VKFTPTLTFVMDALPDTARNIE
  14 VSSFM....G..--KYKTKQGVQGLESAAGFIRSVLAKKLR..LRQCPRLSFVYDESVRDGFSLS
  15 MGSIK....E..--GASLDNAVKALNNAKGFIQSQIIKRIK..VRSTPKLLFVKDDSLSKSFYVN
  16 VSIMP....H..--ENSQEETLAALKASAGFIACQASKDVV..LKYFPDLNFYMEDIFSPQDHIE
  17 YTILN....Q..---DAREITEEVLEHARGHLRSELAKRIK..LFKTPELHFKYDESLERGLNLS
  18 LDCYD....R..---SQIQTVVNAFKKAQGVFSQMLAQNLY..LAKSVKLHFVKDDAIDNALKIE
  19 YTVLN....Q..---DAREITEEVLEHARGHLRSELAKRIK..LFKIPELHFKYDESLERGLNLS
  20 LDCYN....R..---EQIDRVVGAFNQAKGVFSRVLAHNLY..LAKAVQIHFVKDKAIDNAMRIE
  21 FFPFN....T..--KLTFDEIMDALNNSKHAIRNFITNRIN..MKFSPEIRFYYDYGFDNAIKIE
  22 VSIMP....H..--ENSQEETLAALKASAGFIAFQASKDLV..LKYFPDLNFYVEDIFSPQDHIE
  23 YTIHS....T..-LASDNQKAQIGLEKATGTIKRELGKNLT..MYKIPDLQFVKDESIEYGNKID
  24 VLSSD....H..-------KILSKLKKAEGLIRQFVLQASG..WFKCPKLSFVLDDSLEKQLRLD
  25 VLSSD....H..-------KILSKLKKAEGLIRQFVLQASG..WFKCPKLSFVSDNSLEKQLRLD
  26 YSLLS....N..-LASDNEKAATALKKATGLFKSELAKRMT..IFKIPDLTFAKDESVEYGSKID
  27 LSIFP....S..---EKSSEILESIKHNTKTIRYDLGQQVRtqLRKIPDLTFYIDDSLDYLENID
  28 LDAHK....R..---ESMLKVLENVNKVSGLLRSKLAAEWT..SYKVPELRFVIDETIDYANHID
  29 WMCRG....D..GDS----EIVDFLEESKHQIRRRVEESIG..I-TCPEVKFIGDKALLMEQEMD
  30 VSVFG....D..--DRGKDVAIAGLKSKAKYVRSELGKRMK..LRLTPEVRFIEDEAMERG----
  31 VSAIG....A..----DMPELLDALTHARGRLQRELSAHVR..MRRTPTLEF-------------


      0       120        
     |         |        
   1 NLVTNVVREDEKKHVEESN
   2 NLVTSVVKHDEERRVNPDD
   3 NLVTNVVREDEKKHVEES-
   4 NLVTNVIKNDVERQVNP--
   5 RLLREVKQ-----------
   6 TLIHELHSEK---------
   7 NLLNNLPQAIATEDLEDDD
   8 QLLVQLGYDPLKDKEK---
   9 NLLWQIQEK----------
  10 ELLARARAA----------
  11 NLLWQIQEK----------
  12 ELLARARAA----------
  13 DLLDKARQSDEK-------
  14 RKIDRLES-----------
  15 KLIEGLN------------
  16 SLLLKIAEQDKKLTHNNN-
  17 ALIDQVAAEK---------
  18 QIINSL-------------
  19 ALIDQVAAEK---------
  20 SIINSLKKSK---------
  21 ELLKN--------------
  22 SLLLKIAEQDK--------
  23 EMLRNLDK-----------
  24 AIFNEIAKGKD--------
  25 AIFNEIAKGKD--------
  26 EIL----------------
  27 RLLN---------------
  28 ELFKKIKQ-----------
  29 KLFREADYG----------
  30 -------------------
  31 -------------------